QC Report

	general
Report generated at	2021-08-31 23:04:27
Title	scrt-1_OP802_earlyembryonic_1_2
Description	gevirl
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	23845944	16856422	21878946
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	23435064	16560087	21558994
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.3	98.2	98.5
Paired Reads	23845944	16856422	21878946
Paired Reads (QC-failed)	0	0	0
Read1	11922972	8428211	10939473
Read1 (QC-failed)	0	0	0
Read2	11922972	8428211	10939473
Read2 (QC-failed)	0	0	0
Properly Paired Reads	23286842	16442268	21160062
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.7	97.5	96.7
With itself	23389014	16526030	21507768
With itself (QC-failed)	0	0	0
Singletons	46050	34057	51226
Singletons (QC-failed)	0	0	0
% Singleton	0.2	0.2	0.2
Diff. Chroms	10549	7459	12837
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10624122	7488748	9734528
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2022130	1199714	1785998
Paired Optical Duplicate Reads	216842	116645	231569
% Duplicate Reads	19.0334	16.020200000000003	18.346999999999998

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1
Total Reads	17203984	12578068	15897060
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17203984	12578068	15897060
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17203984	12578068	15897060
Paired Reads (QC-failed)	0	0	0
Read1	8601992	6289034	7948530
Read1 (QC-failed)	0	0	0
Read2	8601992	6289034	7948530
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17203984	12578068	15897060
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	17203984	12578068	15897060
With itself (QC-failed)	0	0	0
Singletons	0	0	0
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Fragments	10569392	7450640	9664368
Distinct Fragments	8577081	6269949	7908718
Positions with Two Read	1429254	893417	1282715
NRF = Distinct/Total	0.811502	0.841532	0.818338
PBC1 = OneRead/Distinct	0.803272	0.836363	0.810062
PBC2 = OneRead/TwoRead	4.820507	5.869549	4.994526

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	75368	1211
N1	46127	564
N2	36038	522
Np	75902	1244
N optimal	75902	1244
N conservative	75368	1211
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0070852351130453	1.0272502064409579
Self Consistency Ratio	1.2799544924801598	1.0804597701149425
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Number of raw peaks

	rep1	rep2
Number of peaks	119577	120001

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	75.0	68.0	82.0	82.0
25 percentile	300.0	270.0	316.0	316.0
50 percentile (median)	300.0	270.0	316.0	316.0
75 percentile	300.0	270.0	316.0	316.0
Max size	300.0	270.0	392.0	392.0
Mean	299.8556244093764	269.88404263297804	297.10128617363347	315.68950752285843

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	9984870	7046054
Estimated Fragment Length	185	165
Cross-correlation at Estimated Fragment Length	0.723969092347927	0.66303797183476
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7236299	0.661825
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.718668	0.6553245
NSC (Normalized Strand Cross-correlation coeff.)	1.007376	1.01177
RSC (Relative Strand Cross-correlation coeff.)	1.068357	1.186597

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.39915848174701746	0.3911825008653074
Synthetic AUC	0.4984609619189256	0.4981940507303385
X-intercept	0.01839266289432452	0.01899543925830564
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5721006357095096	0.573753280839895
Synthetic Elbow Point	0.5023835077975531	0.5016256812412538
JS Distance	0.0399688782225215	0.05084277984395789
Synthetic JS Distance	0.1818082329749922	0.18885568864490537
% Genome Enriched	41.960819536341226	41.99495025099049
Diff. Enrichment	8.165143784945256	9.33301071164745
CHANCE Divergence	0.06940208054536397	0.07936879442429996

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.5007865038702664	0.4950528968359847	0.42236007659621166	0.39177638409968846	0.42572615738308056	0.39682882935598696	0.48678271060704614	0.4986847783356231	0.49891310377135867

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.3487043807458264	0.22965593318384858	0.1818294351723969	0.3513834439614839

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.011981444394765008	0.006771164167555608	0.006753739922538183	0.012179080205756138

For spp raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates